15-55497816-GGA-AG

Variant names:

• chr15-55497816-GGA-AG
• rs1060503095
• NM_130810.4:c.165_167delTCCinsCT

Variant summary

Our verdict is Pathogenic. The variant received 12 ACMG points: 12P and 0B. PVS1 PM2 PP5_Moderate

The NM_130810.4(DNAAF4):​c.165_167delTCCinsCT​(p.Pro56SerfsTer2) variant causes a frameshift, missense change. The variant was absent in control chromosomes in GnomAD project. Variant has been reported in ClinVar as Pathogenic (★). Variant results in nonsense mediated mRNA decay.

• Frequency: Genomes: not found (cov: 32)
• Consequence: DNAAF4 NM_130810.4 frameshift, missense
• Clinical Significance: Pathogenic criteria provided, single submitter P:1
• Conservation: PhyloP100: 7.08
• Publications: 0 publications found

Genes affected

DNAAF4 (HGNC:21493): (dynein axonemal assembly factor 4) This gene encodes a tetratricopeptide repeat domain-containing protein. The encoded protein interacts with estrogen receptors and the heat shock proteins, Hsp70 and Hsp90. An homologous protein in rat has been shown to function in neuronal migration in the developing neocortex. A chromosomal translocation involving this gene is associated with a susceptibility to developmental dyslexia. Mutations in this gene are associated with deficits in reading and spelling. Alternative splicing results in multiple transcript variants. Read-through transcription also exists between this gene and the downstream cell cycle progression 1 (CCPG1) gene. [provided by RefSeq, Mar 2011]

DNAAF4-CCPG1 (HGNC:43019): (DNAAF4-CCPG1 readthrough (NMD candidate)) This locus represents naturally occurring read-through transcription between the neighboring dyslexia susceptibility 1 candidate 1 (DYX1C1) and cell cycle progression 1 (CCPG1) genes on chromosome 15. The read-through transcript is a candidate for nonsense-mediated mRNA decay (NMD), and is thus unlikely to produce a protein product. [provided by RefSeq, Mar 2011]

ACMG classification

Our verdict: Pathogenic. The variant received 12 ACMG points.

• PVS1: Loss of function variant, product undergoes nonsense mediated mRNA decay. LoF is a known mechanism of disease.
• PM2: Very rare variant in population databases, with high coverage
• PP5: Variant 15-55497816-GGA-AG is Pathogenic according to our data. Variant chr15-55497816-GGA-AG is described in ClinVar as Pathogenic. ClinVar VariationId is 410963.Status of the report is criteria_provided_single_submitter, 1 stars.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_130810.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	DNAAF4	NM_130810.4	MANE Select	c.165_167delTCCinsCT	p.Pro56SerfsTer2	frameshift missense	Exon 3 of 10	NP_570722.2
	DNAAF4	NM_001033560.2		c.165_167delTCCinsCT	p.Pro56SerfsTer2	frameshift missense	Exon 3 of 9	NP_001028732.1
	DNAAF4	NM_001033559.3		c.165_167delTCCinsCT	p.Pro56SerfsTer2	frameshift missense	Exon 3 of 9	NP_001028731.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	DNAAF4	ENST00000321149.7	TSL:1 MANE Select	c.165_167delTCCinsCT	p.Pro56SerfsTer2	frameshift missense	Exon 3 of 10	ENSP00000323275.3
	DNAAF4	ENST00000448430.6	TSL:1	c.165_167delTCCinsCT	p.Pro56SerfsTer2	frameshift missense	Exon 2 of 8	ENSP00000403412.2
	DNAAF4	ENST00000457155.6	TSL:1	c.165_167delTCCinsCT	p.Pro56SerfsTer2	frameshift missense	Exon 2 of 8	ENSP00000402640.2

Frequencies

GnomAD3 genomes Cov.: 32

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome Cov.: 32

ClinVar

Significance: Pathogenic

Submissions summary: Pathogenic:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Pathogenic:1

Apr 15, 2019

Labcorp Genetics (formerly Invitae), Labcorp

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

For these reasons, this variant has been classified as Pathogenic. Loss-of-function variants in DNAAF4 are known to be pathogenic (PMID: 23872636). This variant has not been reported in the literature in individuals with DNAAF4-related disease. ClinVar contains an entry for this variant (Variation ID: 410963). This variant is not present in population databases (ExAC no frequency). This sequence change creates a premature translational stop signal (p.Pro56Serfs*2) in the  DNAAF4 gene. It is expected to result in an absent or disrupted protein product.

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
PhyloP100		7.1

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs1060503095; hg19: chr15-55790014;